Pittsburgh Post-Gazette Article (Dec. 9, 2005)
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Publications
This is a list of publications originating from our group.
- Qinglan Li, Alexandros Labrinidis, and Panos K. Chrysanthis. ViP: a User-centric View-based Annotation Framework for Scientific Data, Proc. of the 20th International Conference on Scientific and Statistical Database Management (SSDBM'08), 295-312, Hong Kong, China, July 2008.
- S. Ta'asan and R. Gandlin, BioLogic: A Mathematical Modeling Framework for immunologists. A chapter book in Systems Biology, Editor Ivan Maly, Humana Press, Methods in Molecular Biology series, (in press)
- Bauer, A, Marino, S, Hogue, I and Kirschner, D. The effects of HIV-1 on latent TB infection. (in press) Mathematical Modelling of Natural Phenomena 2008.
- Hogue, I, Bajaria, S, Qin, S, Fallert, B, Reinhart, T and Kirschner, D. The Dual Role of Dendritic cells in the Immune Response to HIV-1 Infection, Journal of General Virology, 89(Pt 9):2228-39, 2008.
- Chang, S, Linderman, JL and Kirschner, D. The effect of multiple polymorphisms on antigen presentation and susceptibility to M. tuberculosis infection, Infection and Immunity, pp 3221–3232, 2008.
- Soumya, D. Chakravarty, SD, Zhu, G, Tsai, MC, Mohan, VP, Marino, S, Kirschner, DE, Huang, B, Flynn, J and John Chan. Tumor Necrosis Factor Blockade in Chronic Murine Tuberculosis Leads to Granuloma Disorganization and Enhanced Pulmonary Inflammation Infection and Immunity, 76(3): 916–926, 2008.
- Marino; S, Hogue; IB, Ray; CJ, Denise Kirschner. A Methodology For Performing Global Uncertainty And Sensitivity Analysis In Systems Biology Journal of Theoretical Biology, 254(1), 2008
- Ray, JCJ, Chan, J and Kirschner, D. Competing requirements for macrophage function contribute to intracellular survival of Mycobacterium tuberculosis (in press) The Journal of Theoretical Biology, 2008
- Carlson PE Jr., Horzempa J, Neophytou P, Labrinidis, and GJ Nau: Detection of the host cytosolic environment is essential for Francisella survival 2008 PLosPathogen under revision.
- T. H. Lin, N. Kaminski and Z. Bar-Joseph. Alignment and Classification of Time Series Gene Expression in Clinical Studies. Bioinformatics (ISMB), 24(13):i147-i155, 2008.
- Ernst, Q.K. Beg, K. Kay, G. Balazsi, Z. Oltvai and Z. Bar-Joseph. A Semi-Supervised Method for Predicting Transcription Factor-Gene Interactions in Escherichia coli. PLoS Computational Biology, 4(3): e1000044, 2008 3
- Marino, S, Sud, D, Flynn,J Kirschner, D. Differences in reactivation of tuberculosis induced from anti-TNF treatments are based on bioavailability in granulomatous tissue. PLOS Computational Biology, 3(10): e194, 2007.
- Marino, S, Baretta, E and Kirschner, D. The role of delays in innate and adaptive immunity to intracellular bacteria infections Mathematical Biosciences and Engineering, 261-286, Volume 4,2007.
- HL Plessner, PL Lin, T Khono, J Louie, D Kirschner, J Chan and JL Flynn. Neutralization of TNF by antibody but not by TNF receptor fusion molecule exacerbates chronic murine tuberculosis Journal of Infectious Diseases, 195(11):1643-50, 2007.
- T. Riggs, A. Walts, N. Perry, J. Lynch, J Linderman, M. Miller, D. Kirschner. Interaction of Tcells with Dendritic cells in the lymph node T-zone: random vs. chemotactic movement. (about to be submitted).
- Morel PA, S Ta'asan, BF Morel, DE Kirschner and JL Flynn. New insights into mathematical modeling of the immune system. 2006. Immunol. Res. 36:157-166
- Mahony S, Auron PE, Benos PV: DNA Familial Binding Profiles Made Easy: Comparison of Various Motif Alignment and Clustering Strategies. PLoS Comput Biol 2007, 3(3):e61;
- J. Ernst, O. Vainas, C.T. Harbison, I. Simon and Z. Bar-Joseph. Reconstructing dynamic regulatory maps Molecular Systems Biology, 3:74, 2007
- R. Gandlin and S. Ta'asan: Modeling Large Scale Biological Systems Using Partial Temporal Measurements. SIAM J. on Scientific Computing (submitted)
- Lu Y, Mahony S, Benos PV, Rosenfeld R, Simon I, Breeden LL, Bar-Joseph Z: Combined analysis reveals a core set of cycling genes. Genome Biol 2007, 8(7):R146.
- Mahony S, Benos PV: STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, 35(Web Server issue):W253-258
- Mahony S, Auron PE, Benos PV: Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics 2007, 23(13):i297-304
- Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, et al: Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007, 447(7141):167-177
- Mahony S, Corcoran DL, Feingold E, Benos PV: Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Genome Biol 2007, 8(5):R84.
- N. Kaminski and Z. Bar-Joseph. A patient-gene model for temporal expression profiles in clinical studies. Journal of Computational Biology, 14(3), pp 324-338, 2007.
- Y. Shi, M. Klustein, I. Simon, T. Mitchell, Z. Bar-Joseph. Continuous hidden process model for time series expression experiments. Bioinformatics (Proceedings of ISMB 2007), 23(13), pp i459-i467, 2007.